mvdbeek
556ee003ae
Fix parse_values_from_file tool and tests
2019-05-14 00:14:34 +02:00
mvdbeek
8337f55e21
Fix tests for bed2gff
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and use single-quotes for path, remove deprecated inpterpreter
attribute.
Fixes https://jenkins.galaxyproject.org/job/docker-main-tools-py3/248/
2019-05-08 17:45:10 +02:00
John Chilton
b59fc06d22
Remove GFF headers during conversion.
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Fixes #7771 .
2019-05-08 17:44:52 +02:00
Nicola Soranzo
c9f63ac2f8
Simplify code
2019-04-29 19:22:11 +01:00
mvdbeek
0c1334fea0
Fix grouping1 with modern sort, fix test data
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This tool currently fails with `sort: multi-character tab '$\\\\t'\n`
(https://jenkins.galaxyproject.org/view/All/job/docker-main-tools/lastCompletedBuild/testReport/test.functional/test_toolbox_pytest/test_tool_Grouping1_test_1_/ ).
This also removes test data that should be included in
galaxy-test-data instead (xref
https://github.com/galaxyproject/galaxy-test-data/pull/5 ),
and adds a test file that was missing from
https://github.com/galaxyproject/galaxy/pull/7205 .
2019-04-29 17:38:10 +02:00
mvdbeek
f444b03b90
Add a expression tool that creates parameters from input file
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This tool allows parsing text, integer, float and boolean parameters
from a input dataset.
This closes #7774
2019-04-23 12:11:16 +02:00
vahid
3798a3d124
Commented-out cloudbridge requirement for the cloud/send tool.
2019-04-12 08:46:46 -04:00
Nicola Soranzo
a12db037ca
Merge branch 'release_19.01' into dev
2019-04-11 00:43:45 +01:00
Björn Grüning
78ad61506f
Merge pull request #7699 from mvdbeek/fix_sort_tool_too_stringent
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[19.01] Only check for exit code on actual sort command
2019-04-10 10:33:36 +02:00
Nicola Soranzo
aa008a650b
Restore check_call for sed
2019-04-09 20:26:27 +01:00
Dannon Baker
c521decf32
Specify profile and look for exit codes for genomespace tool -- warnings cause failures otherwise
2019-04-09 13:34:06 -04:00
mvdbeek
68423aa361
Cleanup sorter.py
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Feed open output file to Popen instead of using stdout redirection in
command string.
2019-04-09 15:35:21 +02:00
mvdbeek
45a0ff6173
Only check for exit code on actual sort command
2019-04-09 14:02:10 +02:00
Dannon Baker
3366a5805b
Specify profile and look for exit codes for genomespace tool -- warnings cause failures otherwise
2019-04-09 07:24:05 -04:00
Dannon
e705758410
Merge pull request #7647 from blankenberg/genomespace-importer-fix
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Fix genomespace_importer tool
2019-04-08 15:38:05 -04:00
mvdbeek
54b9609896
Merge branch 'release_19.01' into dev
2019-04-08 18:29:11 +02:00
mvdbeek
77e7464c51
Detect errors using exit_code for sort tool
2019-04-06 10:00:27 +02:00
Daniel Blankenberg
6e7edd0cb9
Fix genomespace_importer tool_type
2019-04-02 17:35:11 -04:00
vahid
1aa19ec99b
Update cloud imports to adhere with cloudbridge interface changes.
2019-03-22 14:02:48 -07:00
John Chilton
574cc22a08
Merge branch 'release_19.01' into dev
2019-02-26 14:28:20 -05:00
mvdbeek
47ed81feb9
Remove unreachable print statement
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I don't think an exception could ever occur here.
2019-02-26 12:06:07 +01:00
John Chilton
00652f0b3a
Merge pull request #7205 from bernt-matthias/topic/grouping-w-emptycells
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group: don't remove empty cells at the begin/start of lines
2019-02-14 14:53:34 -05:00
Nicola Soranzo
d5a406cef7
Fix errors reported by new flake8 3.7.3
2019-01-31 13:47:21 +00:00
Nicola Soranzo
9207b56eeb
Fix "occured" typo everywhere
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Fix https://github.com/galaxyproject/galaxy/issues/7264
2019-01-24 12:09:57 +00:00
Nicola Soranzo
c58f9acf7f
Merge branch 'release_19.01' into dev
2019-01-21 14:00:46 +00:00
mvdbeek
8d99791afb
Fix data_source tools on python 3
2019-01-18 12:13:13 +01:00
bernt@informatik.uni-leipzig.de
bc86e37d85
groupby: reenabled tests and added some, more bugfix
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- make script exit with code 1 in case of error
- removed one more strip
- adapted tool syntax to best practices
2019-01-12 16:13:23 +01:00
M Bernt
b18aa199aa
group: don't remove empty cells at the begin/start of lines
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currently group removes empty cells at the begin and end of lines
additionally the sort command line is changed (hoping that this looks a bit
more obvious)
2019-01-11 14:41:11 +01:00
mvdbeek
d5520c9cf2
Add python to Count1 tool requirements
2019-01-08 11:21:31 +01:00
John Chilton
bf550da2af
Merge pull request #6684 from nsoranzo/deprecate_param_size
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Deprecate `size` attribute of `<param/>` and remove it from tools
2018-12-12 10:51:28 -05:00
John Chilton
d06718ef24
Merge pull request #6577 from bernt-matthias/topic/grouping-wreplace
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improved grouping tool
2018-12-12 10:45:53 -05:00
John Chilton
7a10f5ce0e
Merge pull request #6998 from qiagu/join1
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Change join two dataset output format to tabular
2018-11-15 17:27:47 +01:00
Qiang Gu
cf86049c0c
update help of joiner two datasets tool
2018-11-13 15:40:51 -08:00
Marius van den Beek and qiagu
aaf49d6d06
Update tools/filters/joiner.xml
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Co-Authored-By: qiagu <36086881+qiagu@users.noreply.github.com >
2018-11-09 12:31:31 -08:00
Qiang Gu
d2f01b3d00
Update joiner.xml
2018-11-09 10:33:59 -08:00
Qiang Gu
880605f17d
change join two dataset output format to auto
2018-11-09 09:48:23 -08:00
Enis Afgan
2f2153292b
Merge pull request #6583 from VJalili/cloud_download_tool
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Send data to cloud
2018-11-06 16:36:19 -05:00
Enis Afgan
566ffaf9d5
Update send tool help text
2018-11-05 15:53:47 -05:00
John Chilton
f035d642ce
Merge pull request #6844 from jmchilton/compressed_types_and_extra_files
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Infrastructure/API Support for Composite Uploads/Downloads
2018-11-01 10:57:09 -04:00
vahid
6c07a0370d
Update description on send tool wrapper.
2018-10-31 10:33:03 -07:00
vahid
341f7d6372
Update output label & tool name to compose a more intuitive log label.
2018-10-31 10:31:48 -07:00
vahid
43e5a1828d
In Cloud send tool: surround error raising blocks of code in try-catch.
2018-10-29 11:05:46 -07:00
vahid
7433e2640b
Extend the help section and refactor Authz to Cloud Authorization.
2018-10-28 12:09:23 -07:00
vahid
39bdb67273
Make duplicate object timestamp shorter and use _ instead of -.
2018-10-28 11:39:47 -07:00
vahid
6f56ff10b9
Remove @ & msec from send tool timestamp.
2018-10-28 11:11:51 -07:00
vahid
ef70f20a58
Swap authz_id and bucket; bucket is the first parameter now.
2018-10-28 10:07:50 -07:00
vahid
e30460049f
Remove _ and capitalize each work in "overwrite_existing".
2018-10-28 10:04:34 -07:00
vahid
a236c64ea7
Repalce "sys.exc_info" with "Exception as e" in cloud Send tool wrapper.
2018-10-25 20:48:06 -07:00
vahid
b72e08e8b8
Merge and resolve conflicts.
2018-10-25 19:07:33 -07:00
vahid
d4d659a851
Replace the hardcoded msg with the exception msg in the cloud send tool.
2018-10-25 13:23:18 -07:00
mvdbeek